add name-tree command and fix --free-loss cost matrix

Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
2026-08-16 13:11:06 +02:00
parent 8615da59a8
commit eee71430a4
14 changed files with 1444 additions and 82 deletions
@@ -46,6 +46,7 @@ nav:
      - dump: usage/dump.md
      - annotate: usage/annotate.md
      - phylo: usage/phylo.md
+      - name-tree: usage/name-tree.md
      - unitig: usage/unitig.md
      - estimate: usage/estimate.md
      - reindex: usage/reindex.md